Analysis of gene copy number in esophageal patient-derived tumor xenografts.

2020 ◽  
Vol 38 (15_suppl) ◽  
pp. e13648-e13648
Author(s):  
Ekaterina A. Lukbanova ◽  
Natalya N. Timoshkina ◽  
Evgeniy N. Kolesnikov ◽  
Mikhail A Kozhushko ◽  
Sergei Kit ◽  
...  
Keyword(s):  
Esophageal Cancer ◽  
Copy Number ◽  
Cancer Biology ◽  
Clonal Selection ◽  
Gene Copy ◽  
Normal Donor ◽  
Relative Copy Number ◽  
Copy Numbers ◽  
Tumor Tissues ◽  
Pdx Models

e13648 Background: Patient-derived tumor xenograft (PDX) models are a valuable resource for studying cancer biology and antitumor drug evaluation. The suitability of tumor models in vivo depends on how accurately they mimic a human disease and reproduce the histotype and molecular genetic features of a human tumor. The purpose of the study was to create a PDX model of human cancer and analyze its characteristics. Methods: PDX models of esophageal cancer were obtained by transplanting a tumor fragment from a patient with esophageal squamous cell carcinoma to the BALB/c Nude athymic mice (n = 10 for one PDX generation). Preservation of the tumor histotype was confirmed histologically (hematoxylin and eosin staining). 5 PDX were generated. An analysis of the relative copy number of the YAP1 and KDM6A genes (Real-Time qPCR) in xenograft and donor tumor tissues was performed in each generation. Results: A decrease in the copy numbers of the YAP1 and KDM6A genes by 3.8 and 2.2 times, respectively, was observed in PDX tumor samples (F3 generation) compared to normal donor tissues (p < 0.05). This trend maintained in F4 and F5 generation PDX samples. No changes in the copy numbers of the YAP1 and KDM6A genes were detected in PDX tumor samples in F1 and F2 generations. A cluster analysis (Hierarchical Clustering, Euclidean distance) demonstrated that samples of the first and second generations of esophageal cancer PDX models were closest to the patient tumor tissues in gene copy numbers. Conclusions: Later generations of esophageal cancer PDX models are characterized by changes in the genes copy numbers due to changes in the tumor and clonal selection. Early PDX generations better reproduce genetic, molecular and morphological features of tumors.

Relative gene copy numbers in various patterns of cervical cancer growth.

2020 ◽  
Vol 38 (15_suppl) ◽  
pp. e18029-e18029
Author(s):  
Natalya N. Timoshkina ◽  
Natalia A. Petrusenko ◽  
Vera P. Nikitina ◽  
Diana A. Spiridonova ◽  
Ekaterina V. Verenikina ◽  
...  
Keyword(s):  
Cervical Cancer ◽  
Copy Number ◽  
Gene Dosage ◽  
Total Sample ◽  
Gene Copy ◽  
Relative Copy Number ◽  
Genomic Changes ◽  
Copy Numbers ◽  
Cyp1a1 Gene ◽  
Gene Copy Numbers

e18029 Background: Numerous studies on cervical cancer confirm an important role of specific genomic changes in the onset and development of cervical intraepithelial neoplasia and their effect on the progression of cervical cancer. Solid tumors are characterized by genomic changes leading to a change in the DNA sequence copy number. The purpose of the study was to reveal changes in the relative copy number of the ESR1, ESR2, GPER1, STS, SULT1A1, SULT1E1, CYP1A1, CYP1A2 genes responsible for the reception and metabolism of estrogens in cervical tissues in endophytic and exophytic patterns of tumor growth in order to find predictive markers of malignancy. Methods: The study included 40 patients aged 28-65 years with cervical cancer of endophytic (n = 20) and exophytic (n = 20) growth patterns. Eligibility criteria included a morphologically confirmed cervical squamous cell cancer T1b-2aN0M0, stage I-II. The Thermo Scientific GeneJET FFPE DNA Purification Kit was used for the DNA extraction from FFPE blocks of tumor and healthy tissues. DNA concentrations were measured on the Qubit 2.0 fluorimeter (Invitrogen, USA) using the Quant-iT dsDNA High-Sensitivity (HS) Assay Kit (Invitrogen, USA). Results: The relative copy number of the GPER1, SULT1A1, CYP1A1 genes in tumor samples increased (p < 0.05) compared with normal tissues in the total sample of patients diagnosed with cervical cancer. In contrast to the total sample, an increase in the SULT1A1 gene dosage did not reach a statistically significant level in any group (p = 0.242 and p = 0.157); the copy number of the GPER1 locus significantly increased only in the group with the endophytic growth pattern (p = 0.040), as well as the CYP1A2 gene dosage (p = 0.025). Patients of 36-55 years with endophytic tumors showed a statistically significant (p < 0.05) increase in the GPER1 and CYP1A1 gene copy numbers with the rates of 41.7% and 66.7%, respectively, as well as an increased amplification of the CYP1A2 gene in 41.67% of patients. In women of 56-75 years with endophytic tumors, an increase in the copy numbers of the ESR2, GPER1, SULT1A1 genes was observed with a frequency of 50%, 100% and 75%, respectively. Patients aged 20-35 and 36-55 years with exophytic tumors showed a statistically significant (p < 0.05) increase in the CYP1A1 gene copy numbers in 33.33% and 45.45%, respectively. Conclusions: The results suggest the use of the GPER1, SULT1A1 and CYP1A1 gene copy numbers as biomarkers of cervical tumors.

scholarly journals Nuclear-cytoplasmic balance: whole genome duplications induce elevated organellar genome copy number

2021 ◽  
Author(s):  
Matheus Fernandes Gyorfy ◽  
Emma R Miller ◽  
Justin L Conover ◽  
Corrinne E Grover ◽  
Jonathan F Wendel ◽  
...  
Keyword(s):  
Copy Number ◽  
Nuclear Genome ◽  
Plant Genome ◽  
Whole Genome ◽  
Genome Copy ◽  
Relative Copy Number ◽  
Organellar Genome ◽  
Plastid Genomes ◽  
Copy Numbers ◽  
Genome Copy Number

The plant genome is partitioned across three distinct subcellular compartments: the nucleus, mitochondria, and plastids. Successful coordination of gene expression among these organellar genomes and the nuclear genome is critical for plant function and fitness. Whole genome duplication events (WGDs) in the nucleus have played a major role in the diversification of land plants and are expected to perturb the relative copy number (stoichiometry) of nuclear, mitochondrial, and plastid genomes. Thus, elucidating the mechanisms whereby plant cells respond to the cytonuclear stoichiometric imbalance that follow WGDs represents an important yet underexplored question in understanding the evolutionary consequences of genome doubling. We used droplet digital PCR (ddPCR) to investigate the relationship between nuclear and organellar genome copy numbers in allopolyploids and their diploid progenitors in both wheat and Arabidopsis. Polyploids exhibit elevated organellar genome copy numbers per cell, largely preserving the cytonuclear stoichiometry observed in diploids despite the change in nuclear genome copy number. To investigate the timescale over which cytonuclear stoichiometry may respond to WGD, we also estimated organellar genome copy number in Arabidopsis synthetic autopolyploids and in a haploid-induced diploid line. We observed corresponding changes in organellar genome copy number in these laboratory-generated lines, indicating that at least some of the cellular response to cytonuclear stoichiometric imbalance is immediate following WGD. We conclude that increases in organellar genome copy numbers represent a common response to polyploidization, suggesting that maintenance of cytonuclear stoichiometry is an important component in establishing polyploid lineages.

Abstract P613: Absolute Gene Quantification Of Intrarenal Renin-angiotensin System Components Using Droplet Digital PCR Analysis

Hypertension ◽  
2016 ◽  
Vol 68 (suppl_1) ◽  
Author(s):  
Ryousuke Satou ◽  
Akemi Katsurada ◽  
Kayoko Miyata ◽  
Andrei Derbenev ◽  
Andrea Zsombok
Keyword(s):  
Copy Number ◽  
System Analysis ◽  
Renin Angiotensin System ◽  
Digital Pcr ◽  
Droplet Digital Pcr ◽  
Gene Copy ◽  
Angiotensin System ◽  
Renin Angiotensin ◽  
Copy Numbers ◽  
Intrarenal Ras

The intrarenal renin-angiotensin system (RAS) has been shown to play crucial roles in the development of hypertension and RAS associated kidney injury including diabetic nephropathy. Although some circulating RAS components are filtered into kidneys and contribute to the regulation of intrarenal RAS activity, evaluating expression levels of RAS components in the kidney is important to elucidate the mechanisms underlying intrarenal RAS activation. Digital PCR is a new technique that has been established to quantify absolute target gene levels, which allows for comparisons of different gene levels. Thus, this study was performed to establish profiles of absolute gene copy numbers for intrarenal RAS components in wild-type (WT) rats, WT and streptozotocin (STZ)-induced diabetic mice. Male Sprague-Dawley rats (N=5) and male C57BL/6J mice were used in this study. The mice were subjected to either control (N=5) or STZ (200 mg/kg, N=4) injection. Seven days after STZ injection, copy numbers of renal cortical angiotensinogen (AGT), angiotensin-converting enzyme (ACE), ACE2, angiotensin type 1 receptor a (AT1a), and AT2 mRNA were determined by a droplet digital PCR. Since (pro)renin proteins produced by juxtaglomerular cells are secreted to circulating system, analysis of renin mRNA was excluded from this evaluation. In the renal cortex of WT rats, the copy number of AGT was higher than other measured RAS components (AGT: 719.2±46.6, ACE: 116.0±14.9, ACE2: 183.6±21.5, AT1a: 196.0±25.2 copies in 1 ng total RNA). AT2 levels were lower than other components (0.068±0.01 copies). In WT mice, ACE exhibited the highest copy number in the components (AGT: 447.2±29.0, ACE: 1662.4±61.2, ACE2: 676.8±41.5, AT1a: 867.0±16.8, AT2: 0.049±0.01 copies). Although STZ-induced diabetes did not change ACE2 and AT1a, ACE levels were reduced (765.5±98.1 copies) and AT2 levels were augmented (0.10±0.01 copies) as previously demonstrated. Accordingly, the absolute quantification by digital PCR established precise gene profiles of intrarenal RAS components, which will provide rationales for targeting the each component in future studies. Furthermore, the results indicate that the high sensitive assay accurately quantifies rare target genes including intrarenal AT2.

Shared DNA-based copy number with divided methylation changes differentiate and clinically associate early stage pancreatic cancer tumors.

2021 ◽  
Vol 39 (3_suppl) ◽  
pp. 434-434
Author(s):  
Eva Chao ◽  
Kyaw Lwin Aung ◽  
Qi Xu ◽  
William H. Matsui ◽  
Jeanne Kowalski
Keyword(s):  
Gene Expression ◽  
Pancreatic Cancer ◽  
Overall Survival ◽  
Clinical Outcomes ◽  
Copy Number ◽  
Cancer Biology ◽  
Early Stage ◽  
Molecular Taxonomy ◽  
Unmet Need ◽  
Gene Copy

434 Background: There is no known molecular taxonomy of pancreatic cancer that can guide therapeutic strategies. Understanding the fundamental molecular mechanism underlying pancreatic cancer biology remains an unmet need. We explore the extent to which combinations of DNA-based molecular changes in copy number (CN) and methylation separate early stage PAAD tumors and associated with survival outcomes. Methods: We performed genome-wide combined cluster analyses on DNA-based CN and methylation changes using TCGA data. We examined cluster associations with clinical outcomes by comparing in months (mos), Kaplan--Meier estimated overall survival (OS) and disease-free interval (DFI) using a log-rank test. We performed additional comparisons among CN-Methylation derived clusters with respect to PAAD phenotypes. Results: Using 78 early stage pancreatic cancer tumors from TCGA with CN, methylation and clinical outcomes data, we identified two patient clusters with distinct gene copy number signatures that when combined with three methylation signatures, resulted in three additional clusters. Thus, the same gene CN signature, when combined with different methylation signatures, further differentiated tumors into sub-clusters with varying levels of associations with clinical outcome. Among them, analogous to current gene-expression based subtypes, we also identified an immune-rich subtype that was associated with improved overall survival (n=21, median OS=16mos; DFI=16mos), and an extracellular matrix (ECM)-rich with worse survival (n=19, median OS=12mos; DFI=8mos). Unlike previous expression subtypes, we identified another metabolic-enriched subtype with the same worse median OS and DFI, differentiated by methylation with the ECM-rich subtype. The improved OS cluster had a signature of CN neutral and increased methylation, while the poor cluster had a signature of CN gains and increased methylation among a set of genes distinct from the improved cluster. No significant differences in age, site, microsatellite instability and KRAS status among clusters were noted. Notably, in a multivariable model that included gene expression-based subtypes, only our DNA-level subtypes remained significantly associated with overall survival. Conclusions: While RNA-level changes often display large variations, DNA-level changes are more robust. Copy number changes appear to separate tumors into poor and improved prognosis clusters, while methylation appears to inform on the further separation of poor prognosis into various levels. A DNA-based molecular taxonomy for early stage pancreatic cancer could prove invaluable when used in combination with methylation-based circulating tumor DNA assays for clinical trial monitoring of tumor responses.

scholarly journals Photo-Induced Electron Transfer Real-Time PCR for Detection ofPlasmodium falciparum plasmepsin 2Gene Copy Number

2018 ◽  
Vol 62 (8) ◽  
Author(s):  
Samaly Santos Souza ◽  
Mariangela L'Episcopia ◽  
Carlo Severini ◽  
Venkatachalam Udhayakumar ◽  
Naomi W. Lucchi
Keyword(s):  
Electron Transfer ◽  
Real Time ◽  
Real Time Pcr ◽  
Copy Number ◽  
Gene Copy ◽  
Content Type ◽  
Copy Numbers ◽  
Ofplasmodium Falciparum ◽  
Photo Induced Electron Transfer ◽  
Gene Copy Numbers

ABSTRACTPiperaquine is an important partner drug used in artemisinin-based combination therapies (ACTs). An increase in theplasmepsin 2and3gene copy numbers has been associated with decreased susceptibility ofPlasmodium falciparumto piperaquine in Cambodia. Here, we developed a photo-induced electron transfer real-time PCR (PET-PCR) assay to quantify the copy number of theP. falciparumplasmepsin 2gene (PfPM2) that can be used in countries whereP. falciparumis endemic to enhance molecular surveillance.

scholarly journals Salivary amylase gene copy number and its association with fasting and postprandial glucose response

2020 ◽  
Vol 79 (OCE2) ◽  
Author(s):  
Mary Farrell ◽  
Emily Sonestedt ◽  
Anne Raben ◽  
Juscelino Tovar ◽  
Stina Ramne ◽  
...  
Keyword(s):  
Observational Study ◽  
Copy Number ◽  
Fasting Glucose ◽  
Postprandial Glucose ◽  
Gene Copy ◽  
Amylase Gene ◽  
Salivary Amylase ◽  
Glucose Levels ◽  
Copy Numbers ◽  
Meal Study

AbstractIntroductionWhen compared to other primates, humans elicit a large variation in the copy number for the salivary amylase gene, AMY1. This variation can range from 2 to 17 copies. The AMY1 gene is responsible for coding for salivary amylase, an enzyme needed to catalyze the hydrolysis of starch molecules into smaller sugars. AMY1 copy number correlates with the amount and activity of salivary amylase. Few studies have investigated the effect of amylase copy number on fasting and postprandial glucose levels. The aim was first to investigate the association between AMY1 copy numbers and fasting glucose in an observational study, and secondly to investigate the difference in postprandial effect of high-starch meals in individuals with either high or low AMY1 copy numbers.Materials and methodsFor the observational study, we used data from 436 participants from the Malmö Offspring Study (MOS) cohort whom have been genotyped for AMY1. For the meal study (conducted during May 2019), we used genotype-based-recall to recruit 24 participants from the observational study of the MOS cohort: 12 with low AMY1 copy number (from the lowest 20%) and 12 with high AMY1 copy numbers (from the highest 20%). Each subject will be served a breakfast meal of white wheat bread on two separate test days: one containing 40 g and the other containing 80 g of carbohydrates (mainly starch). Blood samples will then be taken at various time points to investigate postprandial glucose and insulin responses.ResultsWhen using linear regression analyses adjusting for age and sex, no significant association between AMY1 copy number and fasting glucose was observed (p = 0.23). However, there was a difference (p = 0.05) in fasting glucose levels between the lowest (2–4 copy numbers: 5.31 mmol/L; 95% CI: 5.13–5.50) and highest (10–16 copy numbers: 5.57 mmol/L; 95% CI: 5.39–5.75) copy number groups. The results for the meal study will be obtained in June 2019 and be presented at the conference.DiscussionOur findings of higher fasting glucose among the group with more than 10 AMY1 copy numbers is the first study to find this and needs to be replicated in other populations.

scholarly journals Plasmodium copy number variation scan: gene copy numbers evaluation in haploid genomes

2016 ◽  
Vol 15 (1) ◽  
Author(s):  
Johann Beghain ◽  
Anne-Claire Langlois ◽  
Eric Legrand ◽  
Laura Grange ◽  
Nimol Khim ◽  
...  
Keyword(s):  
Copy Number Variation ◽  
Copy Number ◽  
Gene Copy ◽  
Copy Numbers ◽  
Number Variation ◽  
Gene Copy Numbers

scholarly journals Copy Number Variations of CEP63, FOSL2 and PAQR6 Serve as Novel Signatures for the Prognosis of Bladder Cancer

2021 ◽  
Vol 11 ◽  
Author(s):  
Zhao Cai ◽  
Huang Chen ◽  
Jingqiao Bai ◽  
Yang Zheng ◽  
Jianhui Ma ◽  
...  
Keyword(s):  
Bladder Cancer ◽  
Prognostic Factors ◽  
High Risk ◽  
Copy Number ◽  
Copy Number Variations ◽  
Invasive Bladder Cancer ◽  
Gene Copy ◽  
Muscle Invasive Bladder Cancer ◽  
Copy Numbers ◽  
Muscle Invasive

BackgroundFinding effective prognostic signatures is of great urgency due to the high risk of recurrence and progression of bladder cancer (BC). Although a lot of genetic alterations are involved in the carcinogenesis, none of them were referred in the current risk group stratifications. In this study, we aimed to find significant copy number variations (CNVs) to predict prognosis for BC patients.MethodsCNVs with high aberration frequencies in BC were explored by array-based comparative genomic hybridization in 65 tumor samples. Candidates were validated in independent groups of BC tumor samples (n=219) and urine samples (n=123). 3D digital PCR was applied for detecting accurate gene copy numbers in BC urine. In order to explore the prognostic value of candidate CNVs, all enrolled patients were followed up for the disease-free survival (DFS). Cox proportional hazards regression analysis was performed to find the independent prognostic factors for DFS.ResultsCNVs of CEP63, FOSL2 and PAQR6 with high aberration frequencies (67.7%, 56.9% and 60.0%, respectively) were found in BC tumors. Copy numbers of CEP63, FOSL2 and PAQR6 were gained in 219 tumor samples. CNVs of CEP63 and FOSL2 were correlated with advanced tumor stage and high grade. Retrospective analysis (median follow-up time: 69 months) revealed that CNVs of CEP63 and FOSL2 were independent prognostic factors for DFS of non-muscle-invasive bladder cancer (NMIBC) patients, while CNVs of FOSL2 and PAQR6 were independent prognostic factors for DFS of muscle-invasive bladder cancer (MIBC) patients. Models for predicting DFS were constructed based on CNVs of three genes. Patients with high prognostic indexes tended to have poor DFS. Prognostic index can also help to identify those with worse outcomes among high risk NMIBC patients. Copy number gains of CEP63 and FOSL2 in urine were found to be significantly correlated with poor DFS of NMIBC patients.ConclusionsCNVs of CEP63, FOSL2 and PAQR6 were capable of predicting DFS and may serve as promising signatures for prognosis of BC.

scholarly journals High levels of copy number variation of ampliconic genes across major human Y haplogroups

2017 ◽  
Author(s):  
Danling Ye ◽  
Arslan Zaidi ◽  
Marta Tomaszkiewicz ◽  
Corey Liebowitz ◽  
Michael DeGiorgio ◽  
...  
Keyword(s):  
Copy Number Variation ◽  
Y Chromosome ◽  
Copy Number ◽  
Gene Copy Number ◽  
Gene Families ◽  
Digital Pcr ◽  
Gene Copy ◽  
Copy Numbers ◽  
Number Variation ◽  
Gene Copy Numbers

AbstractDue to its highly repetitive nature, the human male-specific Y chromosome remains understudied. It is important to investigate variation on the Y chromosome to understand its evolution and contribution to phenotypic variation, including infertility. Approximately 20% of the human Y chromosome consists of ampliconic regions which include nine multi-copy gene families. These gene families are expressed exclusively in testes and usually implicated in spermatogenesis. Here, to gain a better understanding of the role of the Y chromosome in human evolution and in determining sexually dimorphic traits, we studied ampliconic gene copy number variation in 100 males representing ten major Y haplogroups world-wide. Copy number was estimated with droplet digital PCR. In contrast to low nucleotide diversity observed on the Y in previous studies, here we show that ampliconic gene copy number diversity is very high. A total of 98 copy-number-based haplotypes were observed among 100 individuals, and haplotypes were sometimes shared by males from very different haplogroups, suggesting homoplasies. The resulting haplotypes did not cluster according to major Y haplogroups. Overall, only three gene families (DATZ, RBMY, TSPY) showed significant differences in copy number among major Y haplogroups, and the haplogroup of an individual could not be predicted based on his ampliconic gene copy numbers. Finally, we found a significant correlation between copy number variation and individual’s height (for three gene families), but not between the former and facial masculinity/femininity. Our results suggest rapid evolution of ampliconic gene copy numbers on the human Y, and we discuss its causes.

EGFR mutations (muts), IHC and FISH status, and chromosome 7 gene copy number combined with pAkt expression as potential predictors of survival in non-small cell lung cancer (NSCLC) patients (pts) treated with gefitinib (GEF)

2006 ◽  
Vol 24 (18_suppl) ◽  
pp. 7182-7182 ◽  
Author(s):  
V. M. Villaflor ◽  
L. Buckingham ◽  
M. Gale ◽  
J. Coon ◽  
A. M. Mauer ◽  
...  
Keyword(s):  
Copy Number ◽  
Gene Copy Number ◽  
Chromosome 7 ◽  
Egfr Mutations ◽  
Gene Copy ◽  
Double Positive ◽  
Specific Pcr ◽  
Copy Numbers ◽  
Kaplan Meier ◽  
Nsclc Patients

7182 Background: EGFR and pAkt expression by immunohistochemistry (IHC), muts, and FISH status have been identified as possible molecular predictors for GEF efficacy in NSCLC (Cappuzzo, et. al, JNCI, 2005). The goal of this study was to independently evaluate these findings regarding survival (surv), and to assess the predictive value of mean chromosome 7 copy number/cell (C7). Methods: 150 consecutive Expanded Access Trial pts with >1 week GEF therapy were included for analysis. IHC (present vs not detected) was performed for 87 pts, and 58 pts were analyzed for muts by SSCP, mut-specific PCR, and sequencing. Tissue from 81 pts was evaluated for EGFR and C7 gene copy numbers by fluorescence in situ hybridization (FISH). Results: 150 pts (77 female, 73 male; median (md) age 67; 85 adenocarcinoma) received GEF; md follow-up was 5.8 months (mo). Overall response was 8% (2 CR, 10 PR); 56 pts had stable disease. Md Kaplan-Meier surv was 5.9 mo. IHC revealed that 47/87 pts (54%) had EGFR+, and 36/75 pts (48%) had pAkt + tumors. pAkt+ pts had significantly (sig) longer surv than pAkt− pts (11.4 vs 5.8 mo, p < .05). High polysomy was seen in 36/81 pts (44%) who were designated FISH+; 45 pts were FISH−. EGFR IHC and FISH positivity were not sig associated with surv. C7 was defined as low (<3.6, 63 pts) or high (≥3.6, 18 pts); md surv was 6.6 and 17.1 mo, respectively, p < .01. Muts were found in 17/58 tumors (29%). Md surv for pts with and without muts was 23.8 and 7.9 mo, respectively, p < .07. EGFR IHC− pAkt− pts (18 pts) had sig shorter surv than 57 pts with any pos value (4.7 vs 8.8 mo, p < .02). Double-positive pts had sig longer surv than pts with any neg value. Conclusions: These findings resemble but do not duplicate those reported by Cappuzzo, et al. Additionally, high C7, alone or combined with pAKT, may be an important predictor for GEF efficacy in NSCLC. Further studies of C7, a technically simple and reproducible FISH assay, are warranted. [Table: see text] [Table: see text]

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